Cyanobacterial blooms, a harmful consequence of water eutrophication, necessitate efficient algal removal strategies. This study synthesized magnetic bentonite and kaolinite via co-precipitation by loading nano-Fe₃O₄ onto clay minerals. The materials were characterized using SEM, FTIR, and XRD: single-factor experiments and response surface methodology (Box-Behnken design) optimized parameters for algae removal. Optimal conditions included a 1:1 ratio of magnetic clay minerals to cationic polyacrylamide (CPAM), pH 2, 10 min stirring (150 rpm), and dosages of 0.8 g/L (magnetic bentonite) and 0.4 g/L (magnetic kaolinite). Further refinement via response surface analysis yielded 92.13% algal cell removal with magnetic bentonite at 0.206 g/L, 12.9 min stirring, and 170.6 rpm. Mechanistic studies (Zeta potential, SEM, particle size analysis) indicated that electrostatic adsorption between algae and magnetic clays formed flocs, subsequently captured by CPAM networks. This rapid, efficient process highlights the potential of magnetic clay-CPAM composites for treating eutrophic, algae-laden waters. The findings offer a technical reference for sustainable water remediation.